Lyme disease is an emerging public challenge due to its increasing incidence, expanding geographic range, and heterogeneous clinical manifestations that may involve the skin, nervous system, heart, and joints. The disease is caused by spirochetes of the genus ?Borreliella ?(previously referred to as the ?Borrelia burgdorferi sensu lato group), a diverse group that contains over 20 species, four of which commonly affect humans. Clinical disease varies on the basis of the infecting species, yet the specific microbial factors that mediate these effects are not known. To identify such genes, the candidate and co-mentors have begun conducting genomic association studies of ?Borreliella ?spp. from patients. These preliminary studies have revealed a number of promising candidate loci that are associated with distinct clinical manifestations of Lyme disease. This proposal is a career development award that provides a pathway to independence and includes a 24-month mentored phase followed by a 24-month independent phase. In Aim 1, the candidate will conduct whole genome sequencing using hybrid assembly of short- and long-read sequences to produce finished assemblies for hundreds of ?Borreliella ?spp. genomes from patients and perform evolutionary and population genetic analyses to identify variants that may influence clinical manifestations. In Aim 2, the candidate will conduct genetic association studies of Lyme disease spirochetes to identify microbial lipoproteins associated with distinct clinical manifestations. As a part of this Aim, the candidate will develop imputation methods for publicly available genomic data and also develop target capture methods that enable whole-genome sequencing without microbial culture. In Aim 3, the candidate will characterize the mechanisms of pathogenesis of a prioritized subset of the newly-identified loci using laboratory models. The candidate is a physician-scientist and current Clinical and Research Fellow in Infectious Disease at Massachusetts General Hospital (MGH) with an interest and background in tick-borne disease pathogenesis and genomics. The proposed training and research plan will take place under the guidance of primary mentor Dr. Pardis Sabeti and secondary mentors Dr. John Leong, Dr. Allen Steere, and Dr. Klemen Strle. The mentor team brings together leading investigators with complementary expertise in microbial genomics (Dr. Sabeti), bacterial pathogenesis (Dr. Leong), and clinical studies of Lyme disease (Dr. Strle and Dr. Steere). The work will be carried out in a supportive, collaborative environment at MGH, the Broad Institute, and Tufts University that will foster training and research. Completion of the proposed plan will position the candidate to lead an independent, NIH-funded research program that performs basic, translational, and clinical studies of Lyme disease and other tick-borne pathogens.